https://github.com/arjunrajlaboratory/RajLabSeqTools
Revision 510a48cb71c018f6afed535d18677686a32cebfe authored by Sydney Shaffer on 12 October 2015, 16:55:45 UTC, committed by Sydney Shaffer on 12 October 2015, 16:55:45 UTC
1 parent 284b48d
Tip revision: 510a48cb71c018f6afed535d18677686a32cebfe authored by Sydney Shaffer on 12 October 2015, 16:55:45 UTC
updated path to data in submission script
updated path to data in submission script
Tip revision: 510a48c
unzipAndCat.sh
#!/bin/bash
EXPERIMENT=$1
for dirname in /home/opadovan/C1_Single_Cell_RNA_Seq-11219209/* ; do
cd $dirname
INPUT=`ls *001_R1*`
SAMPLE=`echo $INPUT | cut -d'_' -f 1`
if [ ! -d $EXPERIMENT/raw ]; then
mkdir $EXPERIMENT/raw
fi
if [ ! -d $EXPERIMENT/raw/$SAMPLE ]; then
mkdir $EXPERIMENT/raw/$SAMPLE
fi
for i in *.gz; do
gunzip -c $i > ${i%.*}
done
FASTQR1=`echo $SAMPLE'_R1.fastq'`
FASTQR2=`echo $SAMPLE'_R2.fastq'`
cat *R1*fastq > $EXPERIMENT/raw/$SAMPLE/$FASTQR1
cat *R2*fastq > $EXPERIMENT/raw/$SAMPLE/$FASTQR2
done
Computing file changes ...